Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012339.1 Kokia drynarioides strain JFW-HI SEQ_127341, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 218470
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 92 characters in sequence are not A, C, G, or T
Found at i:3213 original size:24 final size:24
Alignment explanation
Indices: 3185--3235 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3175 AGAAATAATC
* *
3185 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
3209 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
3233 TTT
1 TTT
3236 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:3547 original size:111 final size:101
Alignment explanation
Indices: 3353--3564 Score: 334
Period size: 111 Copynumber: 2.0 Consensus size: 101
3343 CCCATCATAA
3353 TTTAGAACTCCTAACACTTTTGGAGAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTCGGGT
1 TTTAGAACTCCTAACACTTTTGGAGAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTCGGGT
3418 TTTTGGGGTTTAGTTTTTATCTCCATCTTTTGTACT
66 TTTTGGGGTTTAGTTTTTATCTCCATCTTTTGTACT
3454 NNNNNNNNNNTTTAGAACTCCTAACACTTTTGGAGAATTTAGTGTTTACGTTTTGAGGGTTCTTT
1 ----------TTTAGAACTCCTAACACTTTTGGAGAATTTAGTGTTTACGTTTTGAGGGTTCTTT
3519 ATTTTCGGGTTTTTGGGGTTTAGTTTTTATCTCCATCTTTTGTACT
56 ATTTTCGGGTTTTTGGGGTTTAGTTTTTATCTCCATCTTTTGTACT
3565 ATTTGTTCTT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.48
Consensus pattern (101 bp):
TTTAGAACTCCTAACACTTTTGGAGAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTCGGGT
TTTTGGGGTTTAGTTTTTATCTCCATCTTTTGTACT
Found at i:5314 original size:24 final size:24
Alignment explanation
Indices: 5286--5336 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
5276 AGAAATAATC
* *
5286 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
5310 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
5334 TTT
1 TTT
5337 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:5882 original size:30 final size:30
Alignment explanation
Indices: 5840--5896 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5830 AATAGGATGG
* *
5840 GAGAGGAGTAAAAGTTTTGGG-GGGAAAGT
1 GAGAGGAATAAAACTTTTGGGTGGGAAAGT
5869 GAGAGAGAATAAAACTTTTGGGTGGGAA
1 GAGAG-GAATAAAACTTTTGGGTGGGAA
5897 GTTAAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.21
30 14 0.58
31 5 0.21
ACGTcount: A:0.37, C:0.02, G:0.40, T:0.21
Consensus pattern (30 bp):
GAGAGGAATAAAACTTTTGGGTGGGAAAGT
Found at i:6242 original size:22 final size:21
Alignment explanation
Indices: 6208--6260 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
6198 AATGTTTAAT
*
6208 TTTTTTTTAATTTGACCCTTA
1 TTTTTTTAAATTTGACCCTTA
* *
6229 TTTTTTTAACATTTGATCTTTA
1 TTTTTTTAA-ATTTGACCCTTA
*
6251 ATTTTTTAAA
1 TTTTTTTAAA
6261 AAAAAAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.25, C:0.09, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTTTTAAATTTGACCCTTA
Found at i:12937 original size:30 final size:31
Alignment explanation
Indices: 12903--12962 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12893 TTAAGTGTCA
*
12903 AATTTAAC-TAAAAAATAAAAAATAAAAACC
1 AATTTAACAGAAAAAATAAAAAATAAAAACC
* *
12933 AATTTAACAGAAAAAATAAATATTAAAAAC
1 AATTTAACAGAAAAAATAAAAAATAAAAAC
12963 TAAATTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.22
Consensus pattern (31 bp):
AATTTAACAGAAAAAATAAAAAATAAAAACC
Found at i:14313 original size:16 final size:17
Alignment explanation
Indices: 14292--14326 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
14282 TATTAAATTT
*
14292 AATTAATTAATTTT-TC
1 AATTAAATAATTTTCTC
14308 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
14325 AA
1 AA
14327 CCCAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:18113 original size:10 final size:10
Alignment explanation
Indices: 18088--18135 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
18078 CGTACTTTAC
*
18088 TTTCTTTTTGT
1 TTTCTTTCT-T
18099 TTTCTTTCTT
1 TTTCTTTCTT
18109 TTTCTTTCTT
1 TTTCTTTCTT
* *
18119 TCTCGTTCTT
1 TTTCTTTCTT
*
18129 TCTCTTT
1 TTTCTTT
18136 TTTATTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.00, C:0.21, G:0.04, T:0.75
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:18116 original size:14 final size:14
Alignment explanation
Indices: 18082--18131 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
18072 GTTACTCGTA
18082 CTTTACTTTCTTTTT
1 CTTT-CTTTCTTTTT
*
18097 GTTTTCTTTCTTTTT
1 -CTTTCTTTCTTTTT
**
18112 CTTTCTTTCTCGTT
1 CTTTCTTTCTTTTT
18126 CTTTCT
1 CTTTCT
18132 CTTTTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.57
15 10 0.33
16 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (14 bp):
CTTTCTTTCTTTTT
Found at i:31317 original size:3 final size:3
Alignment explanation
Indices: 31309--31364 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
31299 ACTCGGAACG
* * ** *
31309 AAT AAT AAT AAG AAA AAT AAT GGT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31357 AAT AAT AA
1 AAT AAT AA
31365 AACCTAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:31381 original size:21 final size:18
Alignment explanation
Indices: 31339--31437 Score: 65
Period size: 21 Copynumber: 4.9 Consensus size: 18
31329 TGGTAATAGT
* *
31339 AATAATAATAAT-AATAAT
1 AATAATAA-AATAAAAAAA
31357 AATAATAAAACCTAAAAAATA
1 AATAATAAAA--TAAAAAA-A
31378 AATAATAAAATAAAAAAA
1 AATAATAAAATAAAAAAA
31396 AATTAAATAAACAATTAAATAAAAGA
1 AA-T-AAT-AA-AA-T-AA-AAAA-A
31422 AATAATAAAATAAAAA
1 AATAATAAAATAAAAA
31438 TATTGAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
17 2 0.03
18 11 0.16
19 12 0.18
20 9 0.13
21 13 0.19
22 4 0.06
23 3 0.04
24 5 0.07
25 5 0.07
26 3 0.04
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (18 bp):
AATAATAAAATAAAAAAA
Found at i:31389 original size:12 final size:12
Alignment explanation
Indices: 31339--31439 Score: 65
Period size: 12 Copynumber: 8.6 Consensus size: 12
31329 TGGTAATAGT
31339 AATAATAATAAT-
1 AATAATAA-AATA
31351 AATAATAATAATAA
1 AATAATAA-AAT-A
31365 AACCTAA-AAAATA
1 AA--TAATAAAATA
31378 AATAATAAAATA
1 AATAATAAAATA
31390 AA-AA-AAAATTA
1 AATAATAAAA-TA
*
31401 AATAA-ACAAT-
1 AATAATAAAATA
* *
31411 TA-AATAAAAGA
1 AATAATAAAATA
31422 AATAATAAAATA
1 AATAATAAAATA
31434 AA-AATA
1 AATAATA
31440 TTGAAAAAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
9 2 0.03
10 8 0.11
11 15 0.21
12 35 0.48
13 3 0.04
14 5 0.07
15 2 0.03
16 3 0.04
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:34644 original size:24 final size:24
Alignment explanation
Indices: 34616--34714 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
34606 ACATACAACA
* *
34616 TTAGCTCTCACGAGCCCAGGATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
34640 TTAGCTTTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* **
34664 TTAGCTCTTATGAGCCCTCAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* * *
34688 TTAGCTCTTATGAGCCTAGAATAG
1 TTAGCTCTTACGAGCCCAGAATGG
34712 TTA
1 TTA
34715 ACTAGTATAC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:62808 original size:21 final size:21
Alignment explanation
Indices: 62778--62824 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
62768 GATTAGTTCG
* *
62778 AAGGATAAAAA-AAGAAAGCGC
1 AAGGACAAAAAGAAGAAA-CAC
62799 AAGGACAAAAAGAAGAAACAC
1 AAGGACAAAAAGAAGAAACAC
62820 AAGGA
1 AAGGA
62825 GGAAGGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.64, C:0.11, G:0.23, T:0.02
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAACAC
Found at i:80900 original size:20 final size:20
Alignment explanation
Indices: 80875--80940 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
80865 AAAATTAATT
80875 TAAAATTATTTTTTAAAATA
1 TAAAATTATTTTTTAAAATA
80895 TAAAATTA----TTAAAATTA
1 TAAAATTATTTTTTAAAA-TA
* *
80912 TTATATTATTTTTT-AAATA
1 TAAAATTATTTTTTAAAATA
80931 TAAAATTATT
1 TAAAATTATT
80941 AAAATTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
16 6 0.16
17 8 0.22
19 10 0.27
20 11 0.30
21 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAAATTATTTTTTAAAATA
Found at i:80908 original size:16 final size:16
Alignment explanation
Indices: 80887--80945 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
80877 AAATTATTTT
80887 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
* *
80903 TTAAAATTATTATATTATTT
1 TTAAAA-TA-TA-A-AATTA
*
80923 TTTAAATATAAAATTA
1 TTAAAATATAAAATTA
80939 TTAAAAT
1 TTAAAAT
80946 TATTAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 15 0.45
17 3 0.09
18 4 0.12
19 3 0.09
20 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:80909 original size:9 final size:9
Alignment explanation
Indices: 80887--80952 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
80877 AAATTATTTT
80887 TTAAAA-TA
1 TTAAAATTA
80895 -TAAAATTA
1 TTAAAATTA
80903 TTAAAATTA
1 TTAAAATTA
* *
80912 TTATATTATTT
1 TTA-A-AATTA
*
80923 TTTAAA-TA
1 TTAAAATTA
80931 -TAAAATTA
1 TTAAAATTA
80939 TTAAAATTA
1 TTAAAATTA
80948 TTAAA
1 TTAAA
80953 TATTTTTAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
7 9 0.20
8 5 0.11
9 25 0.54
10 2 0.04
11 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:80931 original size:36 final size:36
Alignment explanation
Indices: 80878--80959 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
80868 ATTAATTTAA
80878 AATTATTTTTTAAAATATAAAATTATTAAAATTATT
1 AATTATTTTTTAAAATATAAAATTATTAAAATTATT
80914 ATATTATTTTTT-AAATATAAAATTATTAAAATTATT
1 A-ATTATTTTTTAAAATATAAAATTATTAAAATTATT
*
80950 AAATATTTTT
1 AATTATTTTT
80960 AACCTCATCG
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
35 8 0.18
36 26 0.59
37 10 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AATTATTTTTTAAAATATAAAATTATTAAAATTATT
Found at i:81270 original size:47 final size:47
Alignment explanation
Indices: 81201--81295 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
81191 AGATTCTAAT
81201 TTTGGATCTTGTGTCTGTGAAATTTTGATCTTCCTTTTTTTAGGTTA
1 TTTGGATCTTGTGTCTGTGAAATTTTGATCTTCCTTTTTTTAGGTTA
81248 TTTGGATCTTGTGTCTGTGAAATTTTGATCTTCCTTTTTTTAGGTTA
1 TTTGGATCTTGTGTCTGTGAAATTTTGATCTTCCTTTTTTTAGGTTA
81295 T
1 T
81296 CTTCAATTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.15, C:0.11, G:0.19, T:0.56
Consensus pattern (47 bp):
TTTGGATCTTGTGTCTGTGAAATTTTGATCTTCCTTTTTTTAGGTTA
Found at i:82650 original size:29 final size:29
Alignment explanation
Indices: 82607--82943 Score: 261
Period size: 29 Copynumber: 11.4 Consensus size: 29
82597 AGAGAATTCG
*
82607 GGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* * *
82636 GGGTAAAAAAGTAATTTTAGG-AAATTTTA
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTA
* *
82665 GGGTTAAAATGTGATTTTGGAAAGGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
82694 GGGTTAAAATGTGATTTTAGG-AAGGTTTAA
1 GGGTTAAAATGTAATTTT-GGAAAAGTTT-A
* * * *
82724 GGGTCATAATGTGATTTTGGAGAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-A
*
82754 GGGTTATAATGTAATTTTAGG-AAAGTTTA
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTA
* **
82783 GAGTTTAAAATGTAATTTTAAAAAAGTTTA
1 G-GGTTAAAATGTAATTTTGGAAAAGTTTA
* **
82813 GGGGTCAAAAAAATAATTTT-GAAGAAGTTTAA
1 -GGGT-TAAAATGTAATTTTGGAA-AAGTTT-A
* ** *
82845 GGGTCAAAATGGGATTTT-GAGAAGTTTGA
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-A
* * * * *
82874 GGGTAAAAATATATTTTTTGAGAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
*
82903 GGGTTAAAATGTAATTTTGGATAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
*
82932 GAGTTCAAAATG
1 GGGTT-AAAATG
82944 GGATTTTTAA
Statistics
Matches: 251, Mismatches: 43, Indels: 27
0.78 0.13 0.08
Matches are distributed among these distances:
28 2 0.01
29 121 0.48
30 103 0.41
31 24 0.10
32 1 0.00
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:82841 original size:31 final size:31
Alignment explanation
Indices: 82795--82853 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
82785 GTTTAAAATG
*
82795 TAATTTTAAAAAAGTTTAGGGGTCAAAAAAA
1 TAATTTTAAAAAAGTTTAAGGGTCAAAAAAA
* *
82826 TAATTTTGAAGAAGTTTAAGGGTCAAAA
1 TAATTTTAAAAAAGTTTAAGGGTCAAAA
82854 TGGGATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (31 bp):
TAATTTTAAAAAAGTTTAAGGGTCAAAAAAA
Found at i:82951 original size:59 final size:57
Alignment explanation
Indices: 82607--82932 Score: 262
Period size: 59 Copynumber: 5.5 Consensus size: 57
82597 AGAGAATTCG
* * *
82607 GGGTTAAAATATAATTTTGGAAAAGTTTA-GGGTAAAAAAGTAATTTTAGGAAATTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGT-AAAATGTAATTTTAGG-AAGTTTA
* * * *
82665 GGGTTAAAATGTGATTTTGGAAAGGTTTAGGGTTAAAATGTGATTTTAGGAAGGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTAAAATGTAATTTTAGGAA-GTTT-A
* * * * * *
82724 GGGTCATAATGTGATTTTGGAGAAGTTTAAGGGTTATAATGTAATTTTAGGAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-AGGGGTAAAATGTAATTTTAGG-AAGTTTA
* ** ** *
82783 GAGTTTAAAATGTAATTTTAAAAAAGTTTAGGGGTCAAAAAAATAATTTTGAAGAAGTTTAA
1 G-GGTTAAAATGTAATTTTGGAAAAGTTTAGGGGT--AAAATGTAATTTT-AGGAAGTTT-A
* ** * * * *
82845 GGGTCAAAATGGGATTTT-GAGAAGTTT-GAGGGTAAAAATATATTTTTTGAGAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG-GGGT-AAAATGTAATTTTAG-GAAGTTTA
*
82903 GGGTTAAAATGTAATTTTGGATAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
82933 AGTTCAAAAT
Statistics
Matches: 215, Mismatches: 39, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
57 2 0.01
58 59 0.27
59 63 0.29
60 56 0.26
61 31 0.14
62 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (57 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTAAAATGTAATTTTAGGAAGTTTA
Found at i:85140 original size:77 final size:78
Alignment explanation
Indices: 84926--85316 Score: 374
Period size: 77 Copynumber: 5.0 Consensus size: 78
84916 TTTTTACATT
* * * ** * ** ** *
84926 GGATGGTTGCAATCTGCCCCAAGCTCGGGGTAATAGATTTACTGATGGTGATCTATCGTAGGCTC
1 GGATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTC
*
84991 GAGGTAAAAGATC
66 GGGGTAAAAGATC
* * * * * *
85004 GAATGGCTACAATCTGCCCTAAGCTCAGGGTAAGAGATTAGCTGAT-GATGATCTGCCCCAAGCT
1 GGATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAG-TGATCTGCCCCAAGCT
*
85068 CGGGGTAAAATATC
65 CGGGGTAAAAGATC
* * * * * * *
85082 GGATGGCT-CAATTTACCCTAGGTTCGGGGTAAGAGATTGGTTGATAGTGATCTACCCCAAGCCC
1 GGATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTC
* *
85146 GGGGTAAAATATT
66 GGGGTAAAAGATC
* * * * * *
85159 GGATGGCTGCAATCTACCCCAAGCTCGGAGTAAGAGATTGACCGATGGTGATCTGCCCCATGAT-
1 GGATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTC
**
85223 TAGGTAAAAGATC
66 GGGGTAAAAGATC
* * * * * *
85236 GAATGGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGTTGATAGTGATTTGCCCCACGCTC
1 GGATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTC
85301 GGGGTAAAAGATC
66 GGGGTAAAAGATC
85314 GGA
1 GGA
85317 ATCTTCAATC
Statistics
Matches: 252, Mismatches: 57, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
77 128 0.51
78 124 0.49
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (78 bp):
GGATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTC
GGGGTAAAAGATC
Found at i:85149 original size:39 final size:39
Alignment explanation
Indices: 85106--85198 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
85096 ACCCTAGGTT
* **
85106 CGGGGTAAGAGATTGG-TTGATAGTGATCTACCCCAAGCC
1 CGGGGTAAGAGATTGGATGGAT-GCAATCTACCCCAAGCC
* * * *
85145 CGGGGTAAAATATTGGATGGCTGCAATCTACCCCAAGCT
1 CGGGGTAAGAGATTGGATGGATGCAATCTACCCCAAGCC
*
85184 CGGAGTAAGAGATTG
1 CGGGGTAAGAGATTG
85199 ACCGATGGTG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
39 40 0.93
40 3 0.07
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (39 bp):
CGGGGTAAGAGATTGGATGGATGCAATCTACCCCAAGCC
Found at i:85268 original size:155 final size:156
Alignment explanation
Indices: 84928--85331 Score: 415
Period size: 155 Copynumber: 2.6 Consensus size: 156
84918 TTTACATTGG
* * *** * * ** * *
84928 ATGGTTGCAATCTGCCCCAAGCTCGGGGTAATAGATTTACTGATGGTGATCTATCGTAGGCTCGA
1 ATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTACCCCAAGCTCGG
* * *
84993 GGTAAAAGATCGAATGGCTACAATCTGCCCTAAGCTCAGGGTAAGAGATTAGCTGATGATGATCT
66 GGTAAAAGATCGAATGGCTACAATCTACCCCAAGCTCAGGGTAAGAGATTAGCCGATGATGATCT
* * * *
85058 GCCCCAAGCTCGGGGTAAAATATCGG
131 GCCCCAAGATCGAGGTAAAAGATCGA
* * * * * *
85084 ATGGCT-CAATTTACCCTAGGTTCGGGGTAAGAGATTGGTTGATAGTGATCTACCCCAAGCCCGG
1 ATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTACCCCAAGCTCGG
* * * * *
85148 GGTAAAATATTGGATGGCTGCAATCTACCCCAAGCTC-GGAGTAAGAGATT-GACCGATGGTGAT
66 GGTAAAAGATCGAATGGCTACAATCTACCCCAAGCTCAGG-GTAAGAGATTAG-CCGATGATGAT
* *
85211 CTGCCCCATGAT-TAGGTAAAAGATCGA
129 CTGCCCCAAGATCGAGGTAAAAGATCGA
* * * *
85238 ATGGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGTTGATAGTGATTTGCCCCACGCTCGG
1 ATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTACCCCAAGCTCGG
*
85303 GGTAAAAGATCGGAAT--CTTCAATCTACCC
66 GGTAAAAGATC-GAATGGCTACAATCTACCC
85332 TTATTGATTA
Statistics
Matches: 199, Mismatches: 45, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
154 32 0.16
155 159 0.80
156 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (156 bp):
ATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTACCCCAAGCTCGG
GGTAAAAGATCGAATGGCTACAATCTACCCCAAGCTCAGGGTAAGAGATTAGCCGATGATGATCT
GCCCCAAGATCGAGGTAAAAGATCGA
Found at i:87366 original size:11 final size:11
Alignment explanation
Indices: 87350--87374 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
87340 TGAACTTCTT
87350 CTATGATTTTC
1 CTATGATTTTC
87361 CTATGATTTTC
1 CTATGATTTTC
87372 CTA
1 CTA
87375 GCTTCAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (11 bp):
CTATGATTTTC
Found at i:97311 original size:30 final size:30
Alignment explanation
Indices: 97272--97634 Score: 278
Period size: 30 Copynumber: 12.2 Consensus size: 30
97262 GAGAATTCGA
97272 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
** *
97302 GGCAAAAATGTAATTTTGG-GAAGTTT-GG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
** * * *
97330 AATTAAAATGTGATTTTGGAGAAGTTTA-C
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
* * *
97359 GGTTAAAATATGATTTTTGG-AAGGTTTA-G
1 GGTTAAAATGT-AATTTTGGAAAAGTTTAGG
* * * *
97388 GGTTAAAATTTGATTTT-AAAGAAGTTTAAG
1 GGTTAAAATGTAATTTTGGAA-AAGTTTAGG
* *
97418 GGTTAAAATGTAATTTTAGAAAAGTTTTA-A
1 GGTTAAAATGTAATTTTGGAAAAG-TTTAGG
* * * *
97448 GGTCAAAATATGATTTTGGGAAAGTTT-GAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG-G
* * ** *
97478 GGTTAAAATATAATTTTGAAAAAAATTATG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
97508 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
** * *
97538 GGTTAAAATGGGATTTTGGAGAAG-TTCGAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG-G
* * *
97568 GGTTAAAATATAATTTTTGAGAAGTTT-GAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG-G
* * *
97598 GGTCAAAATGTAAGTTTGGAGAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
97628 GGTTAAA
1 GGTTAAA
97635 TGGGATTTTT
Statistics
Matches: 262, Mismatches: 57, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
28 21 0.08
29 49 0.19
30 183 0.70
31 9 0.03
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAGG
Found at i:97516 original size:90 final size:88
Alignment explanation
Indices: 97332--97634 Score: 313
Period size: 90 Copynumber: 3.4 Consensus size: 88
97322 AAGTTTGGAA
* * * *
97332 TTAAAATGTGATTTTGGAGAAGTTTACGGTTAAAATATGATTTTTGGAAGGTTT-AGGGTTAAAA
1 TTAAAATGTAATTTTGGAAAAGTTTAAGGTTAAAATATGA-TTTTGGAAAGTTTGAGGGTTAAAA
* * **
97396 TTTGATTTTAAAGAAGTTTAAGGG
65 TATAATTTTAAAGAAAATTAAGGG
* *
97420 TTAAAATGTAATTTTAGAAAAGTTTTAAGGTCAAAATATGATTTTGGGAAAGTTTGAGGGTTAAA
1 TTAAAATGTAATTTTGGAAAAG-TTTAAGGTTAAAATATGATTTT-GGAAAGTTTGAGGGTTAAA
*
97485 ATATAATTTTGAAA-AAAATTATGGG
64 ATATAATTTT-AAAGAAAATTAAGGG
* ** *
97510 TTAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGGGATTTTGGAGAAGTTCGAGGGTTAAA
1 TTAAAATGTAATTTTGGAAAAGTTTA-AGGTTAAAATATGATTTTGGA-AAGTTTGAGGGTTAAA
** ** *
97575 ATATAATTTTTGAGAAGTTTGAGGG
64 ATATAATTTTAAAGAAAATTAAGGG
* * * *
97600 TCAAAATGTAAGTTTGGAGAAGTTTAGGGGTTAAA
1 TTAAAATGTAATTTTGGAAAAGTTTA-AGGTTAAA
97635 TGGGATTTTT
Statistics
Matches: 182, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
88 23 0.13
89 32 0.18
90 124 0.68
91 3 0.02
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (88 bp):
TTAAAATGTAATTTTGGAAAAGTTTAAGGTTAAAATATGATTTTGGAAAGTTTGAGGGTTAAAAT
ATAATTTTAAAGAAAATTAAGGG
Found at i:99918 original size:84 final size:82
Alignment explanation
Indices: 99757--99924 Score: 300
Period size: 82 Copynumber: 2.0 Consensus size: 82
99747 TATGTCCGTT
99757 AAAAATTGATAAATTTGACCAAAAAAATATTAGGGGTTAAATTAATCCAAAAAAAAAAAGATAAA
1 AAAAATTGATAAATTTGACCAAAAAAATATTAGGGGTTAAATTAATCCAAAAAAAAAAAGATAAA
99822 AGGTCAAAGTGACAAAA
66 AGGTCAAAGTGACAAAA
*
99839 AAAAATTGGTAAATTTGACCAAAAAAATATTAGGGGTTAAATTAATCCCNAAAAAAAAAAAGATA
1 AAAAATTGATAAATTTGACCAAAAAAATATTAGGGGTTAAATTAAT-CC-AAAAAAAAAAAGATA
*
99904 AAAGGTCAAAGTGACCAAA
64 AAAGGTCAAAGTGACAAAA
99923 AA
1 AA
99925 GTCAAACATT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
82 45 0.55
83 2 0.02
84 35 0.43
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.20
Consensus pattern (82 bp):
AAAAATTGATAAATTTGACCAAAAAAATATTAGGGGTTAAATTAATCCAAAAAAAAAAAGATAAA
AGGTCAAAGTGACAAAA
Found at i:100244 original size:8 final size:7
Alignment explanation
Indices: 100217--100243 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
100207 TACCTCATCT
100217 TTTTTTC
1 TTTTTTC
100224 TTTTTTC
1 TTTTTTC
100231 TTTTTTC
1 TTTTTTC
100238 TTTTTT
1 TTTTTT
100244 TGAAAAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:102981 original size:33 final size:29
Alignment explanation
Indices: 102938--103032 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 29
102928 AAATTTTCCC
*
102938 ATATTATTTTTTAATTTTTTAAAAATATTTAT
1 ATATT-TTTTTTAA-TATTTAAAAAT-TTTAT
*
102970 ATTATATTTTTTTAATATTTAATAATTTTAT
1 A-TAT-TTTTTTTAATATTTAAAAATTTTAT
*
103001 ATATTTTTTATT--TATTAAAAAAATTTTAT
1 ATATTTTTT-TTAATATT-TAAAAATTTTAT
103030 ATA
1 ATA
103033 GTTATCTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
28 4 0.07
29 18 0.33
30 5 0.09
31 6 0.11
32 10 0.18
33 11 0.20
34 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTTTTTTTAATATTTAAAAATTTTAT
Found at i:124716 original size:14 final size:15
Alignment explanation
Indices: 124697--124729 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
124687 AAATAATTGT
124697 AAAATGAAA-TAGAG
1 AAAATGAAAGTAGAG
*
124711 AAAATGAAAGTAGTG
1 AAAATGAAAGTAGAG
124726 AAAA
1 AAAA
124730 AAAAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (15 bp):
AAAATGAAAGTAGAG
Found at i:150284 original size:29 final size:29
Alignment explanation
Indices: 150240--150308 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
150230 AGTGACTGTT
* *
150240 ATATAACTTTTAAAAATTGAGTGATCAA-A-
1 ATATAA-TTTTAAAAATTAAGGGA-CAATAG
150269 ATATAATTTTAAAAAATTAAGGGACAATAG
1 ATATAATTTT-AAAAATTAAGGGACAATAG
150299 ATATAATTTT
1 ATATAATTTT
150309 CCTTTTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 7 0.20
29 18 0.51
30 10 0.29
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.36
Consensus pattern (29 bp):
ATATAATTTTAAAAATTAAGGGACAATAG
Found at i:151518 original size:36 final size:34
Alignment explanation
Indices: 151445--151521 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 34
151435 AAAATAACTC
* **
151445 TTTAAAATTAAAAATATAAAAATGAATTTTAAAT
1 TTTAAAATTAAAAATATAAAAATGAAATCCAAAT
*
151479 TTTAAAATTATTAAAATATATAAA-GAAATCCAAATT
1 TTTAAAATTA--AAAATATAAAAATGAAATCCAAA-T
151515 TTTAAAA
1 TTTAAAA
151522 AATATGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.28
35 7 0.19
36 19 0.53
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
TTTAAAATTAAAAATATAAAAATGAAATCCAAAT
Found at i:151816 original size:92 final size:90
Alignment explanation
Indices: 151698--151936 Score: 290
Period size: 92 Copynumber: 2.6 Consensus size: 90
151688 AATTATATCG
151698 ATAGTTTAGGTACCA-AGTTGGACATTTTCGAATTACAAGTACTACTTTGGACATTTTATGAAAG
1 ATAGTTTAGGTACCACA-TTGGACATTTTCGAATTACAAGTACTACTTTGGACATTTTATGAAAG
*
151762 TACATGTACCATAATAAAA-CATGTATTA
65 TACATGTACCAT-ATAAAAGCA--CATTA
* * * * * *
151790 ATAGTTTAGGTATCACTTTCGACATTTCCAAATTACAAGTGCTA-TATTGGACATTTTATGAAAG
1 ATAGTTTAGGTACCACATTGGACATTTTCGAATTACAAGTACTACT-TTGGACATTTTATGAAAG
*
151854 TATATGTACCATATAAAAGCACATTA
65 TACATGTACCATATAAAAGCACATTA
* *
151880 ATAGTTTGGGTACCACATTGGACATTTTCGAATTA-AAGGTA-TCACATTGGACATTTT
1 ATAGTTTAGGTACCACATTGGACATTTTCGAATTACAA-GTACT-ACTTTGGACATTTT
151937 CGAATTAAAG
Statistics
Matches: 125, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
89 3 0.02
90 47 0.38
91 7 0.06
92 68 0.54
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (90 bp):
ATAGTTTAGGTACCACATTGGACATTTTCGAATTACAAGTACTACTTTGGACATTTTATGAAAGT
ACATGTACCATATAAAAGCACATTA
Found at i:151925 original size:29 final size:29
Alignment explanation
Indices: 151888--151965 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
151878 TAATAGTTTG
151888 GGTACCACATTGGACATTTTCGAATTAAA
1 GGTACCACATTGGACATTTTCGAATTAAA
*
151917 GGTATCACATTGGACATTTTCGAATTAAA
1 GGTACCACATTGGACATTTTCGAATTAAA
* *
151946 GGTACCATATTAGACATTTT
1 GGTACCACATTGGACATTTT
151966 ATGAAAGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (29 bp):
GGTACCACATTGGACATTTTCGAATTAAA
Found at i:152059 original size:13 final size:13
Alignment explanation
Indices: 152033--152083 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
152023 AGTTTAATAT
* *
152033 TGCTTTTGAGAAG
1 TGCTTTTAAAAAG
152046 TGCTTTTAAAAAG
1 TGCTTTTAAAAAG
* *
152059 TGATTTTAGAAAG
1 TGCTTTTAAAAAG
*
152072 TAC-TTTAAAAAG
1 TGCTTTTAAAAAG
152084 CTTGGGTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (13 bp):
TGCTTTTAAAAAG
Found at i:152490 original size:17 final size:18
Alignment explanation
Indices: 152468--152509 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
152458 CTTAATACAT
152468 TACTTTTGAT-TCAAAAG
1 TACTTTTGATGTCAAAAG
*
152485 TACTTTTTATGTCAAAAG
1 TACTTTTGATGTCAAAAG
*
152503 TGCTTTT
1 TACTTTT
152510 AAAAAGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (18 bp):
TACTTTTGATGTCAAAAG
Found at i:158543 original size:5 final size:5
Alignment explanation
Indices: 158533--158570 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
158523 ATAGACCAGT
158533 AAACA AAACA AAACA AAACA AAACA AAACA AAA-A AAAC
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAAC
158571 CCATAAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:161827 original size:25 final size:24
Alignment explanation
Indices: 161799--161855 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
161789 ATATTTATTA
* *
161799 TTTTAATTATCAATATCTTTATAAT
1 TTTTAAATAT-AATATCTTCATAAT
*
161824 TTTTAAAATATTATATCTTCATAAT
1 TTTT-AAATATAATATCTTCATAAT
161849 TTTTAAA
1 TTTTAAA
161856 ATATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 20 0.71
26 5 0.18
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAATATAATATCTTCATAAT
Found at i:161856 original size:25 final size:25
Alignment explanation
Indices: 161811--161861 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
161801 TTAATTATCA
*
161811 ATATCTTTATAATTTTTAAAATATT
1 ATATCTTCATAATTTTTAAAATATT
161836 ATATCTTCATAATTTTTAAAATATT
1 ATATCTTCATAATTTTTAAAATATT
161861 A
1 A
161862 AATTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATCTTCATAATTTTTAAAATATT
Found at i:162904 original size:2 final size:2
Alignment explanation
Indices: 162897--162928 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
162887 GCTCCGAATA
162897 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
162929 GCAGCGGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:162990 original size:38 final size:38
Alignment explanation
Indices: 162934--163021 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
162924 GAGAGGCAGC
*
162934 GGAAGAA-GGTGGGTGGGAAATGAGCAGTAGGTTTCGA
1 GGAAGAAGGGTGGGAGGGAAATGAGCAGTAGGTTTCGA
162971 GGAAGAAGGGTGGGAGGGAAATGAGCAGTAGGTTTCGA
1 GGAAGAAGGGTGGGAGGGAAATGAGCAGTAGGTTTCGA
163009 GGAAGAAGGGTGG
1 GGAAGAAGGGTGG
163022 AAACTGAGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 7 0.14
38 42 0.86
ACGTcount: A:0.31, C:0.05, G:0.49, T:0.16
Consensus pattern (38 bp):
GGAAGAAGGGTGGGAGGGAAATGAGCAGTAGGTTTCGA
Found at i:168047 original size:21 final size:19
Alignment explanation
Indices: 168021--168061 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
168011 ATTAAAAGAG
168021 TAAAAATATAATAATATTTTA
1 TAAAAA-ATAAT-ATATTTTA
*
168042 TAAAAAATTATATATTTTA
1 TAAAAAATAATATATTTTA
168061 T
1 T
168062 TCTCAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAAATAATATATTTTA
Found at i:168120 original size:9 final size:9
Alignment explanation
Indices: 168108--168133 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
168098 TTACTTAATT
168108 TTAAAAATA
1 TTAAAAATA
168117 TTAAAAATA
1 TTAAAAATA
168126 TTAAAAAT
1 TTAAAAAT
168134 TAAAGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TTAAAAATA
Found at i:172827 original size:9 final size:9
Alignment explanation
Indices: 172792--172841 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
172782 TTTTAGTTTC
172792 TTTTAATAA
1 TTTTAATAA
172801 TTATTAAT-A
1 TT-TTAATAA
*
172810 TTTTTATAA
1 TTTTAATAA
172819 TTTTAATAA
1 TTTTAATAA
*
172828 TTATTCATAA
1 TT-TTAATAA
172838 TTTT
1 TTTT
172842 TAAATAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 4 0.11
9 18 0.51
10 13 0.37
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAATAA
Found at i:172856 original size:19 final size:18
Alignment explanation
Indices: 172797--172862 Score: 53
Period size: 20 Copynumber: 3.5 Consensus size: 18
172787 GTTTCTTTTA
* **
172797 ATAATTATTAATATTTTT
1 ATAATTTTTAATAAGTTT
*
172815 ATAA-TTTTAATAATTATT
1 ATAATTTTTAATAAGT-TT
172833 CATAATTTTTAAATAAGTTT
1 -ATAATTTTT-AATAAGTTT
172853 ATAATATTTT
1 ATAAT-TTTT
172863 GAATCATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 9 0.22
18 6 0.15
19 9 0.22
20 10 0.25
21 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATAATTTTTAATAAGTTT
Found at i:173554 original size:22 final size:21
Alignment explanation
Indices: 173511--173554 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
173501 ATTTTAATAA
*
173511 TTTTATAGTTTTTAAATATTT
1 TTTTATAATTTTTAAATATTT
*
173532 TTTTCATAATTTTTACAT-TTT
1 TTTT-ATAATTTTTAAATATTT
173553 TT
1 TT
173555 ATTTTTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATAATTTTTAAATATTT
Found at i:176802 original size:22 final size:23
Alignment explanation
Indices: 176771--176814 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
176761 AAATAGAGTT
* *
176771 ATATATTTTTATGATA-ATTAAA
1 ATATAATTTTATCATATATTAAA
176793 ATATAATTTTATCATATATTAA
1 ATATAATTTTATCATATATTAA
176815 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATAATTTTATCATATATTAAA
Found at i:177430 original size:22 final size:21
Alignment explanation
Indices: 177405--177464 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
177395 GAAATATTTT
177405 TTTTTTTATTATTTTGCTGCTG
1 TTTTTTTATTATTTTGCTG-TG
* * * *
177427 TTTTTTCACTGTTTTGCTGTT
1 TTTTTTTATTATTTTGCTGTG
177448 TTTTTCTTATTGATTTT
1 TTTTT-TTATT-ATTTT
177465 CCACAATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 6 0.21
22 19 0.66
23 4 0.14
ACGTcount: A:0.08, C:0.10, G:0.12, T:0.70
Consensus pattern (21 bp):
TTTTTTTATTATTTTGCTGTG
Found at i:177986 original size:18 final size:18
Alignment explanation
Indices: 177965--178000 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
177955 GTTAACGGTT
*
177965 AAAATGATTTTAAAAATAA
1 AAAAT-ATTATAAAAATAA
177984 AAAATATTATAAAAATA
1 AAAATATTATAAAAATA
178001 TATATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATATTATAAAAATAA
Found at i:182792 original size:18 final size:18
Alignment explanation
Indices: 182769--182827 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
182759 GAATATCATG
*
182769 CTGGCTTGTAAGAGCATA
1 CTGGCTCGTAAGAGCATA
** *
182787 CTGGCTCGTTTGAGTATA
1 CTGGCTCGTAAGAGCATA
*
182805 CTGTCTCGTAAGAGCATTA
1 CTGGCTCGTAAGAGCA-TA
182824 CTGG
1 CTGG
182828 ATCCCGAAAG
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (18 bp):
CTGGCTCGTAAGAGCATA
Found at i:185604 original size:14 final size:14
Alignment explanation
Indices: 185573--185630 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
185563 CGAAAAAAAG
* *
185573 TCAACAGTCATCGT
1 TCAACAGTCAACGA
*
185587 TCAAC-GATCAACGG
1 TCAACAG-TCAACGA
*
185601 TCAACAGTTAACGA
1 TCAACAGTCAACGA
*
185615 TCAACGGTCAACGA
1 TCAACAGTCAACGA
185629 TC
1 TC
185631 GGTCAATGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 1 0.03
14 34 0.94
15 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (14 bp):
TCAACAGTCAACGA
Found at i:185635 original size:11 final size:11
Alignment explanation
Indices: 185619--185649 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
185609 TAACGATCAA
185619 CGGTCAACGAT
1 CGGTCAACGAT
*
185630 CGGTCAATGAT
1 CGGTCAACGAT
185641 CGGTCAACG
1 CGGTCAACG
185650 GTCAGTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (11 bp):
CGGTCAACGAT
Found at i:185657 original size:22 final size:22
Alignment explanation
Indices: 185619--185680 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
185609 TAACGATCAA
* * * *
185619 CGGTCAACGATCGGTCAATGAT
1 CGGTCAACGGTCAGTCAACGAC
185641 CGGTCAACGGTCAGTC-ACGAC
1 CGGTCAACGGTCAGTCAACGAC
* *
185662 CGATTAACGGTCAGTCAAC
1 CGGTCAACGGTCAGTCAAC
185681 TGTCAGTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (22 bp):
CGGTCAACGGTCAGTCAACGAC
Found at i:185758 original size:15 final size:15
Alignment explanation
Indices: 185728--185761 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
185718 GGTTTTGGAC
185728 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
* *
185743 TTGGTTCACTTTGGT
1 TTGGTTCAATTGGGT
185758 TTGG
1 TTGG
185762 GCTTAAAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.32, T:0.50
Consensus pattern (15 bp):
TTGGTTCAATTGGGT
Found at i:187949 original size:52 final size:52
Alignment explanation
Indices: 187871--187975 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
187861 GGGTTGGGAT
* *
187871 GTGTAATAATTGAAGTTGGGAAAGTAATAGCGTATGCCTTCTAATAGTTGAA
1 GTGTAATAATTGAAGTTGGGAAAGTAATAGCGTATGCCTTCCAACAGTTGAA
187923 GTGTAATAATTGAAGTTGGGAAAGTAATAGCGTATGCCTTCCAACAGTTGAA
1 GTGTAATAATTGAAGTTGGGAAAGTAATAGCGTATGCCTTCCAACAGTTGAA
187975 G
1 G
187976 CTGCATGAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (52 bp):
GTGTAATAATTGAAGTTGGGAAAGTAATAGCGTATGCCTTCCAACAGTTGAA
Found at i:191969 original size:20 final size:20
Alignment explanation
Indices: 191955--192004 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
191945 GAAGTTGTAT
191955 CAGTAGAAGTAAAGTTCTAA
1 CAGTAGAAGTAAAGTTCTAA
* *
191975 CGGTAGAAGTAAATTTCT-A
1 CAGTAGAAGTAAAGTTCTAA
191994 CAGGTAGAAGT
1 CA-GTAGAAGT
192005 CCCAGGGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (20 bp):
CAGTAGAAGTAAAGTTCTAA
Found at i:192197 original size:20 final size:20
Alignment explanation
Indices: 192174--192219 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
192164 TAGGGTATTG
* *
192174 GTAGAACTAAAGTTGTATCA
1 GTAGAACTAAAGTTCTACCA
* *
192194 GTAGAAGTGAAGTTCTACCA
1 GTAGAACTAAAGTTCTACCA
192214 GTAGAA
1 GTAGAA
192220 GTCTCACAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (20 bp):
GTAGAACTAAAGTTCTACCA
Found at i:195290 original size:20 final size:20
Alignment explanation
Indices: 195267--195311 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
195257 AAGGTATCGA
* *
195267 TAGAACTAAAGTTGTATCAG
1 TAGAACTAAAGTTCTACCAG
* *
195287 TAGAAGTGAAGTTCTACCAG
1 TAGAACTAAAGTTCTACCAG
195307 TAGAA
1 TAGAA
195312 GTCTCACTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (20 bp):
TAGAACTAAAGTTCTACCAG
Found at i:196914 original size:2 final size:2
Alignment explanation
Indices: 196907--196933 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
196897 CCTCTTGCAC
196907 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
196934 AGTGATACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:210723 original size:27 final size:28
Alignment explanation
Indices: 210692--210748 Score: 98
Period size: 27 Copynumber: 2.0 Consensus size: 28
210682 TAATATGTTG
210692 GACTATATGAAACT-AAGTTAAGAAACA
1 GACTATATGAAACTAAAGTTAAGAAACA
210719 GACTATATGAAACTACAAGTTAAGAAACA
1 GACTATATGAAACTA-AAGTTAAGAAACA
210748 G
1 G
210749 TCAGTGCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 14 0.50
29 14 0.50
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (28 bp):
GACTATATGAAACTAAAGTTAAGAAACA
Found at i:214297 original size:28 final size:28
Alignment explanation
Indices: 214238--214298 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
214228 TGTTATTGAT
* * * *
214238 TTTTTATTCTTAATTTTCAATTCTCGAT
1 TTTTTAATCTAAATTTTCAATTCTCAAG
214266 TTTTTAATCTAAATTTTCAATT-TCAAAG
1 TTTTTAATCTAAATTTTCAATTCTC-AAG
214294 TTTTT
1 TTTTT
214299 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTAATCTAAATTTTCAATTCTCAAG
Found at i:214330 original size:22 final size:22
Alignment explanation
Indices: 214300--214341 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
214290 AAAGTTTTTT
*
214300 TTTTAATTTTCTTAATCTTTTAG
1 TTTTAATTTTATTAAT-TTTTAG
214323 TTTT-ATTTTATTAATTTTT
1 TTTTAATTTTATTAATTTTT
214342 CGATGACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTAATTTTATTAATTTTTAG
Found at i:215061 original size:15 final size:16
Alignment explanation
Indices: 215041--215070 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
215031 AAAAATTGAT
215041 AAAAATTA-AAAATAA
1 AAAAATTAGAAAATAA
215056 AAAAATTAGAAAATA
1 AAAAATTAGAAAATA
215071 TATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAAATTAGAAAATAA
Found at i:216389 original size:18 final size:18
Alignment explanation
Indices: 216345--216401 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 18
216335 AGAGAAACAT
*
216345 AAAG-AGAAGGATAAAGA
1 AAAGAAGAAGGAAAAAGA
216362 CAAATCGAAGAAGGAAAAAGA
1 -AAA--GAAGAAGGAAAAAGA
*
216383 AAAGAAGAA-GAAAGAGA
1 AAAGAAGAAGGAAAAAGA
216400 AA
1 AA
216402 TATAAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 9 0.26
18 9 0.26
20 4 0.12
21 12 0.35
ACGTcount: A:0.67, C:0.04, G:0.26, T:0.04
Consensus pattern (18 bp):
AAAGAAGAAGGAAAAAGA
Found at i:216550 original size:27 final size:27
Alignment explanation
Indices: 216474--216550 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 27
216464 TAAGGAAACG
* *
216474 GAGAAGAAGAAAGAAGGAAAATATGAGGTT
1 GAGAAGAA-AAAGAA-GAAAA-ATGAAGAT
* * *
216504 GAGGGAGAAAAGGATG-AAAATGAAGAT
1 GA-GAAGAAAAAGAAGAAAAATGAAGAT
216531 GAGAAGAAAAAGAAGAAAAA
1 GAGAAGAAAAAGAAGAAAAA
216551 AGACAAGGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
26 10 0.27
27 12 0.32
28 3 0.08
29 1 0.03
30 6 0.16
31 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.09
Consensus pattern (27 bp):
GAGAAGAAAAAGAAGAAAAATGAAGAT
Found at i:216566 original size:114 final size:114
Alignment explanation
Indices: 216448--216682 Score: 402
Period size: 114 Copynumber: 2.1 Consensus size: 114
216438 AATAATGATA
216448 AGAAAAAGAAAAAAGATAAGGAAACGGAGAAGAAGAAAGAAGGAAAATATGAGGTTGAGGGAGAA
1 AGAAAAAGAAAAAAGATAAGGAAACGGAGAAGAAGAAAGAAGGAAAATATGAGGTTGAGGGAGAA
216513 AAGGATGAAAATG-AAGATGAGAAGAAAAAGAAGAAA-AAAGACAAGGAAG
66 AAGGATGAAAA-GAAAGATGAGAAGAAAAAGAA-AAAGAAAGACAAGGAAG
* *
216562 AGAAAAAGAAAAAAGATAAGGAAATGGAGATGAAGAAAGAAGGAAAATATGAGGTTGAGGGAGAA
1 AGAAAAAGAAAAAAGATAAGGAAACGGAGAAGAAGAAAGAAGGAAAATATGAGGTTGAGGGAGAA
* *
216627 GAGGATGAAGAGAAAGATGAGAAGAAAAAGAAAAAGAAAGACAAGGAAG
66 AAGGATGAAAAGAAAGATGAGAAGAAAAAGAAAAAGAAAGACAAGGAAG
216676 AGAAAAA
1 AGAAAAA
216683 TAAAGAAAAG
Statistics
Matches: 115, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
113 4 0.03
114 111 0.97
ACGTcount: A:0.60, C:0.01, G:0.31, T:0.07
Consensus pattern (114 bp):
AGAAAAAGAAAAAAGATAAGGAAACGGAGAAGAAGAAAGAAGGAAAATATGAGGTTGAGGGAGAA
AAGGATGAAAAGAAAGATGAGAAGAAAAAGAAAAAGAAAGACAAGGAAG
Found at i:216709 original size:81 final size:83
Alignment explanation
Indices: 216623--216779 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 83
216613 AGGTTGAGGG
*
216623 AGAAGAGGATGAAGAGA-AAGATGAGAAGAAAAAGAA-AAAGA-AAGACAAGG-AA-GAGAAAAA
1 AGAAGAAGATGAAGAGACAAGA-GAGAAGAAAAAGAAGAAAGACAAG--AAGGTAAGGAGAAAAA
*
216683 TAAAGAAAAGAAGCATGGTAT
63 GAAAGAAAAGAAGCATGGTAT
* *
216704 AGAAGAAGATGAAGAGACAGGAGAGAAGAAAAAGAAGAAAGACAAGGAGGTTAAGGAGAAAAAGA
1 AGAAGAAGATGAAGAGACAAGAGAGAAGAAAAAGAAGAAAGACAAGAAGG-TAAGGAGAAAAAGA
216769 AAGAAAAGAAG
65 AAGAAAAGAAG
216780 TCAAAAGGTG
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
81 33 0.50
82 8 0.12
83 5 0.08
84 20 0.30
ACGTcount: A:0.61, C:0.03, G:0.31, T:0.06
Consensus pattern (83 bp):
AGAAGAAGATGAAGAGACAAGAGAGAAGAAAAAGAAGAAAGACAAGAAGGTAAGGAGAAAAAGAA
AGAAAAGAAGCATGGTAT
Found at i:216822 original size:24 final size:24
Alignment explanation
Indices: 216769--216827 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
216759 GAGAAAAAGA
216769 AAGAAAAG-AAGTCAAAAGGTGAAG
1 AAGAAAAGAAAG-CAAAAGGTGAAG
* *
216793 AGGAAAAGAAAG-AAAAGGATGATG
1 AAGAAAAGAAAGCAAAAGG-TGAAG
216817 AAGAAATAGAA
1 AAGAAA-AGAA
216828 GATAAGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 6 0.21
24 16 0.55
25 7 0.24
ACGTcount: A:0.61, C:0.02, G:0.29, T:0.08
Consensus pattern (24 bp):
AAGAAAAGAAAGCAAAAGGTGAAG
Found at i:217352 original size:17 final size:17
Alignment explanation
Indices: 217282--217361 Score: 81
Period size: 17 Copynumber: 4.6 Consensus size: 17
217272 GCCCAACAGG
* *
217282 ATTTACATTTATTTTAA
1 ATTTAAATTTATTATAA
* *
217299 AATTAAATTTATTTTAA
1 ATTTAAATTTATTATAA
*
217316 GTTTAAATTTACTTA-AA
1 ATTTAAATTTA-TTATAA
*
217333 ATTTAAATTTATTATGA
1 ATTTAAATTTATTATAA
217350 ATTTAAAGTTTA
1 ATTTAAA-TTTA
217362 AATCTATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
16 3 0.06
17 44 0.83
18 6 0.11
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:217355 original size:34 final size:34
Alignment explanation
Indices: 217295--217361 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
217285 TACATTTATT
*
217295 TTAAAATTAAATTTATTTTAAGTTTAAA-TTTAC
1 TTAAAATTAAATTTATTTGAAGTTTAAAGTTTAC
217328 TTAAAATTTAAATTTATTATGAA-TTTAAAGTTTA
1 TTAAAA-TTAAATTTATT-TGAAGTTTAAAGTTTA
217362 AATCTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 6 0.20
34 17 0.57
35 7 0.23
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
TTAAAATTAAATTTATTTGAAGTTTAAAGTTTAC
Found at i:218128 original size:3 final size:3
Alignment explanation
Indices: 218122--218175 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
218112 TAATTATTTT
218122 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
218170 TAA TAA
1 TAA TAA
218176 ATGGTAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.